3DXN | pdb_00003dxn

Crystal structure of the calcium-dependent kinase from toxoplasma gondii, 541.m00134, kinase domain.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% PEG3350, 0.2 M NaCl, 0.1 M Hepes, 5 % ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.345	α = 90
b = 121.345	β = 90
c = 45.521	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2008-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.17	85.75	99.9	0.087	0.097	10.7	7.3	17797	17780			47.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.25	99.7		0.62	0.62	2.72	7.1	1726

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.17	50	17784	17770	904	99.92	0.232	0.232	0.23	0.22	0.265	0.26	RANDOM	44.574

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.23			-0.23		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.347
r_dihedral_angle_4_deg	15.601
r_dihedral_angle_3_deg	13.494
r_dihedral_angle_1_deg	4.371
r_angle_refined_deg	0.866
r_scangle_it	0.432
r_scbond_it	0.304
r_nbtor_refined	0.291
r_mcangle_it	0.267
r_symmetry_vdw_refined	0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.347
r_dihedral_angle_4_deg	15.601
r_dihedral_angle_3_deg	13.494
r_dihedral_angle_1_deg	4.371
r_angle_refined_deg	0.866
r_scangle_it	0.432
r_scbond_it	0.304
r_nbtor_refined	0.291
r_mcangle_it	0.267
r_symmetry_vdw_refined	0.159
r_nbd_refined	0.157
r_mcbond_it	0.152
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.057
r_symmetry_hbond_refined	0.022
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2021
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.